I can't move anything in my inventory
IMO, PermissionsEx is a better permissions plugin. I suggest you do that first, as then I could help your problem more easily. It would also help if you provide a dump of your "permissions.yml" file so people can see what the error is. I suggest making a local copy of "permissions.yml" and deleting the copy from the server, then starting it up again and checking that fixed it. If it did, the problem resides in your permissions.
Also, make sure that if you deny a global node (ex. -modifyworld.*) and allow a finer global node (ex. modifyworld.blocks.place.[asterisk]), the allowed node has to be above the denied one. Good luck, I hope that helps. :)